Membrane proteins comprise between 15% and 39% of the human proteome and 45% of drugs target these proteins. Membrane proteins are prevalent in the proteomes of pathogenic microorganisms and are the targets of many antimicrobial agents. Membrane proteins play essential roles in pathophysiology and the biology of all organisms. Near atomic resolution structures are required for our understanding of the function of these molecules. X-ray crystallography, electron crystallography, and nuclear magnetic resonance spectroscopy (NMR) are the currently available methods for obtaining high resolution structures of macromolecules, including membrane proteins.
Purified membrane proteins require surfactants, typically detergents, to remain soluble in an aqueous environment. The complex of the membrane protein and the associated detergent molecules (the protein detergent complex, PDC), is the object studied by x-ray crystallography or NMR.
The difficulties of working with membrane proteins are demonstrated by the fact that membrane protein structures represent less than 1% of the total number of protein structures in the Protein Data Bank, despite integral membrane proteins encompassing 15-30% of most genomes [1; 2; 3]. Technical challenges in membrane protein structure determination include expression (to obtain suitable amounts of protein), purification (to obtain suitably stable and functional protein), and sample preparation (to obtain suitable two-dimensional crystals for electron crystallography, three-dimensional crystals for x-ray crystallography, or solutions for NMR spectroscopy).
In preparation for structural (and other) studies, membrane proteins are extracted from their native lipid bilayer environment, and this membrane bilayer is replaced by a membrane-mimetic. The membrane-mimetic solute is almost always a detergent at a concentration above its critical micelle concentration (CMC), where the detergent surrounds the hydrophobic membrane-facing portion of the membrane protein and forms the protein-detergent complex (PDC). PDCs are in equilibrium with detergent micelles and monomers in this solution. The chemical-space of detergents is large, and the solution (and crystallization) properties of a membrane protein are intimately related to the properties of the detergent(s) comprising the PDC [4; 5]. In addition, the function of a membrane protein can be maintained at native or near-native levels or can be completely abrogated, depending upon the detergent composition of the PDC.
Currently, according to the Membrane Proteins of Known Structure database, 231 unique integral membrane protein structures have been solved by x-ray crystallography. The Membrane Protein Data Bank database [6] lists 864 non-unique membrane protein x-ray crystal structures, for which more than fifty different detergents have been used in their solubilization and/or crystallization. These detergents are not equally represented. For example, five detergents, n-dodecyl-β-D-maltopyranoside (DDM); n-decyl-β-D-maltopyranoside (DM); n-nonyl-β-D-glucopyranoside (NG); n-octyl-β-D-glucopyranoside (OG); and n-dodecyl-N,N-dimethylamine-N-oxide (LDAO) have yielded the majority of α-helical membrane protein structures [7].
While this speaks to the utility (and extensive use) of these five detergents, over 40% of the structures solved to date required detergents other than those five. As such, survey of membrane protein stability in “detergent-space” is an important aspect of membrane protein structural biology (and biochemistry).
There are several methods to test detergent solubility of membrane proteins. These methods include: gel filtration; dilution [5]; and the ultracentrifugation dispersity sedimentation assay [8]. Inspection of the gel filtration chromatogram has been routinely used for both soluble and membrane proteins to assess the quality of a protein.
The method of fluorescence-detection size-exclusion chromatography (FSEC) was an advance in gel filtration chromatography of integral membrane proteins [9]. The unique optical signal of a fluorescently-tagged recombinant protein enables that protein to be detected and characterized in a solubilized mixture, prior to purification. Also, the use of fluorescence (versus absorbance) detection increases the sensitivity by several orders of magnitude, requiring less solubilized (or purified) protein for the chromatography analysis. In order to evaluate detergent stability, gel filtration can be performed in either of two ways: 1) the column is equilibrated in the detergent to be tested and the protein is loaded onto the column (“detergent-specific mobile phase”) or 2) the protein is exchanged into a new detergent and then injected onto a column equilibrated with a known “good” detergent for all chromatographic runs (“generic mobile phase”).
The use of the generic mobile phase speeds up the gel filtration runs by eliminating the column washing and equilibration steps for the next detergent. The generic mobile phase method rests upon the assumption that if a protein sample has been exchanged into an incompatible detergent, then a compatible detergent in the mobile phase will not reverse the deleterious effects of that incompatible detergent [9].
Data from our lab suggests that this is not true for all cases, so we do not currently favor the generic mobile phase method. We note that the original FSEC publication [9] utilizes a generic mobile phase; however, fluorescence detection is equally applicable to use of a detergent-specific mobile phase. For the dilution method, concentrated protein is diluted into a new test detergent and the Abs320 nm:Abs280 nm ratio is recorded over time. Because Abs320 nm is indicative of protein aggregation, an increase in this ratio is diagnostic of the protein not being stable in the new detergent [5]. In the ultracentrifugation dispersity sedimentation assay, the protein is concentrated, diluted into the test detergent buffer with three concentration/dilution steps, and finally allowed to incubate overnight. At that point, a sample is taken while the rest of the protein is spun in the ultracentrifuge to pellet any aggregated protein. Another protein sample is taken after ultracentrifugation and both the pre- and post-ultracentrifugation samples are run on SDS-PAGE and compared. Any difference in band intensity between the two samples is indicative of aggregated protein being removed during the intermediate ultracentrifugation step and thus related to detergent stability [8].
These three methods all possess shortcomings. The biggest limitation is that the methods described above are not detergent exchanges, but rather are detergent dilutions (the exception is the single case where the protein is already in the same detergent as that present in the gel filtration mobile phase). This is a problem if the initial detergent is not diluted to a concentration below its CMC or, in the case of gel filtration, if the original detergent's micelles are not separated from the protein-detergent complex (PDC), or if a mixed detergent population exists. In these instances, the presence of the original detergent can “protect” a protein from a destabilizing detergent resulting in false positives.
The original detergent's concentration is of great concern especially when the method utilizes an ultrafiltration concentration step of the protein since detergent micelles typically concentrate along with the protein even when a large molecular weight cut-off (MWCO) is used. Another limitation is that milligram amounts of protein and large amounts of expensive detergent reagents may be necessary, especially if there are a large number of conditions to be tested. Lastly, the time required to perform each method can be long, which usually limits the number of detergents surveyed, especially in the case of gel filtration where only one detergent can be tested at a time.
There is a long felt need in the art for compositions and methods useful as a system for efficiently determining conditions and the proper detergents for membrane proteins from solutions containing a membrane protein in a purified and soluble state. The present invention satisfies these needs.